Data source downloader for Funcotator.
Category Variant Evaluation and Refinement
Overview
Tool to download the latest data sources for Funcotator. Created by jonn on 8/23/18.FuncotatorDataSourceDownloader specific arguments
This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
Argument name(s) | Default value | Summary | |
---|---|---|---|
Optional Tool Arguments | |||
--arguments_file |
[] | read one or more arguments files and add them to the command line | |
--extract-after-download |
false | Extract the data sources to a sibling folder after they have been downloaded. | |
--gcs-max-retries -gcs-retries |
20 | If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection | |
--gcs-project-for-requester-pays |
"" | Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. | |
--germline |
false | Download the latest pre-packaged datasources for germline functional annotation. | |
--help -h |
false | display the help message | |
--output -O |
null | Output location for the data sources. | |
--overwrite-output-file |
false | Overwrite output file if it exists already. | |
--somatic |
false | Download the latest pre-packaged datasources for somatic functional annotation. | |
--validate-integrity |
false | Validate the integrity of the data sources after downloading them using sha256. | |
--version |
false | display the version number for this tool | |
Optional Common Arguments | |||
--gatk-config-file |
null | A configuration file to use with the GATK. | |
--QUIET |
false | Whether to suppress job-summary info on System.err. | |
--tmp-dir |
null | Temp directory to use. | |
--use-jdk-deflater -jdk-deflater |
false | Whether to use the JdkDeflater (as opposed to IntelDeflater) | |
--use-jdk-inflater -jdk-inflater |
false | Whether to use the JdkInflater (as opposed to IntelInflater) | |
--verbosity |
INFO | Control verbosity of logging. | |
Advanced Arguments | |||
--showHidden |
false | display hidden arguments |
Argument details
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
--arguments_file / NA
read one or more arguments files and add them to the command line
List[File] []
--extract-after-download / -extract-after-download
Extract the data sources to a sibling folder after they have been downloaded.
boolean false
--gatk-config-file / NA
A configuration file to use with the GATK.
String null
--gcs-max-retries / -gcs-retries
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
int 20 [ [ -∞ ∞ ] ]
--gcs-project-for-requester-pays / NA
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.
String ""
--germline / -germline
Download the latest pre-packaged datasources for germline functional annotation.
Exclusion: This argument cannot be used at the same time as somatic, testing-override-path-for-datasources-sha256, testing-override-path-for-datasources
.
boolean false
--help / -h
display the help message
boolean false
--output / -O
Output location for the data sources.
File null
--overwrite-output-file / -overwrite-output-file
Overwrite output file if it exists already.
boolean false
--QUIET / NA
Whether to suppress job-summary info on System.err.
Boolean false
--showHidden / -showHidden
display hidden arguments
boolean false
--somatic / -somatic
Download the latest pre-packaged datasources for somatic functional annotation.
Exclusion: This argument cannot be used at the same time as germline, testing-override-path-for-datasources-sha256, testing-override-path-for-datasources
.
boolean false
--tmp-dir / NA
Temp directory to use.
String null
--use-jdk-deflater / -jdk-deflater
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
--use-jdk-inflater / -jdk-inflater
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
--validate-integrity / -validate-integrity
Validate the integrity of the data sources after downloading them using sha256.
boolean false
--verbosity / -verbosity
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
- ERROR
- WARNING
- INFO
- DEBUG
LogLevel INFO
--version / NA
display the version number for this tool
boolean false
GATK version 4.0.12.0 built at 23-45-2019 03:45:45.
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